In order to clarify the effects of crop rotation and continuous cropping on the diversity of microbial communities, enzyme activities and physicochemical properties of flue-cured tobacco (JI-Tobacco IX variety) rhizosphere soil, a field experiment was conducted with three treatments of tobacco continuous cropping (N-N), maize-tobacco rotation (Z-N), and soya bean-tobacco rotation (G-N), the nutrients and enzyme activities were measured, the structure and diversity of microbial communities of the rhizosphere soil were analyzed using the high-throughput sequencing, and the economic traits of tobacco leaves were determined. The results showed that rotation cropping (Z-N and G-N) enhanced soil organic matter and total nitrogen, while N-N enriched soil available potassium and phosphorus. Soil urease activity under G-N and acid phosphatase activity under Z-N performed best. Z-N had the highest Chao1 and Shannon indexes in both soil bacteria and fungi, and the highest relative abundance of Aspergillus phylum and Acidobacterium phylum of bacteria and Stamenomycetes phylum of fungi. The highest relative abundance at the genus level was found in bacterial Bacillus spp. under Z-N soil and in fungal Aspergillus spp. under G-N. PCA analysis showed that there were significant differences in soil bacterial and fungal community structures under different treatments. Spearman's correlation analysis revealed that there was a significant correlation between soil physicochemical indexes and the community structures of bacteria and fungi at the genus level. Under different cropping patterns, Z-N had the best economic traits of tobacco, with highest yields, production values and the ratio of top-grade tobacco leaves, while N-N was the lowest. In conclusion, Z-N comprehensively performed better and could be a new rotation pattern in tobacco-planting areas in Jilin Province, and further study is needed to explore its mechanism and methods in soil improvement.